Chapter 4 Community composition
4.1 Taxonomy overview
4.1.1 Stacked barplot
genome_counts_filt %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
left_join(., genome_metadata, by = join_by(genome == genome)) %>% #append genome metadata
left_join(., sample_metadata, by = join_by(sample == sample)) %>% #append sample metadata
filter(count > 0) %>% #filter 0 counts
ggplot(., aes(x=sample,y=count, fill=phylum, group=phylum)) + #grouping enables keeping the same sorting of taxonomic units
geom_bar(stat="identity", colour="white", linewidth=0.1) + #plot stacked bars with white borders
scale_fill_manual(values=phylum_colors) +
facet_nested(. ~ treatment + trial, scales="free") + #facet per day and treatment
guides(fill = guide_legend(ncol = 1)) +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1),
axis.title.x = element_blank(),
panel.background = element_blank(),
panel.border = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(linewidth = 0.5, linetype = "solid", colour = "black")) +
labs(fill="Phylum",y = "Relative abundance",x="Samples")
### Phylum relative abundances
phylum_summary <- genome_counts_filt %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>%
left_join(sample_metadata, by = join_by(sample == sample)) %>%
left_join(genome_metadata, by = join_by(genome == genome)) %>%
group_by(sample,phylum) %>%
summarise(relabun=sum(count))
phylum_summary %>%
group_by(phylum) %>%
summarise(mean=mean(relabun, na.rm=T),sd=sd(relabun, na.rm=T)) %>%
arrange(-mean) %>%
tt()| phylum | mean | sd |
|---|---|---|
| p__Bacteroidota | 0.5429264135 | 0.0839814443 |
| p__Bacillota_A | 0.2053118388 | 0.0504873476 |
| p__Bacillota | 0.0820882796 | 0.0332609240 |
| p__Bacillota_C | 0.0492489327 | 0.0142741661 |
| p__Spirochaetota | 0.0482278851 | 0.0467236412 |
| p__Cyanobacteriota | 0.0310050620 | 0.0165287926 |
| p__Pseudomonadota | 0.0172699714 | 0.0170094305 |
| p__Campylobacterota | 0.0162452268 | 0.0388594354 |
| p__Patescibacteria | 0.0022213343 | 0.0014395316 |
| p__Thermoplasmatota | 0.0019390776 | 0.0018321268 |
| p__Verrucomicrobiota | 0.0010490684 | 0.0022355045 |
| p__Bacillota_B | 0.0010095801 | 0.0006944021 |
| p__Elusimicrobiota | 0.0007469834 | 0.0010942911 |
| p__Fibrobacterota | 0.0007103462 | 0.0011143593 |
phylum_arrange <- phylum_summary %>%
group_by(phylum) %>%
summarise(mean=mean(relabun)) %>%
arrange(-mean) %>%
select(phylum) %>%
pull()
phylum_summary %>%
filter(phylum %in% phylum_arrange) %>%
mutate(phylum=factor(phylum,levels=rev(phylum_arrange))) %>%
ggplot(aes(x=relabun, y=phylum, group=phylum, color=phylum)) +
scale_color_manual(values=phylum_colors[rev(phylum_arrange)]) +
geom_jitter(alpha=0.5) +
theme_minimal() +
theme(legend.position="none") +
labs(y="Phylum",x="Relative abundance")
4.2 Taxonomy boxplot
4.2.1 Family
family_summary <- genome_counts_filt %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
left_join(sample_metadata, by = join_by(sample == sample)) %>% #append sample metadata
left_join(., genome_metadata, by = join_by(genome == genome)) %>% #append genome metadata
group_by(sample,family) %>%
summarise(relabun=sum(count))
family_summary %>%
group_by(family) %>%
summarise(mean=mean(relabun, na.rm=T),sd=sd(relabun, na.rm=T)) %>%
arrange(-mean) %>%
tt()| family | mean | sd |
|---|---|---|
| f__Bacteroidaceae | 0.4700966396 | 0.1019283906 |
| f__Lachnospiraceae | 0.1171338702 | 0.0452596418 |
| f__Treponemataceae | 0.0408387686 | 0.0440444319 |
| f__Gastranaerophilaceae | 0.0296035799 | 0.0160991852 |
| f__Selenomonadaceae | 0.0289746313 | 0.0095722337 |
| f__Oscillospiraceae | 0.0259606214 | 0.0106720994 |
| f__UBA660 | 0.0256112036 | 0.0182125645 |
| f__UBA932 | 0.0230420425 | 0.0092838271 |
| f__Ruminococcaceae | 0.0180292427 | 0.0088616619 |
| f__Muribaculaceae | 0.0178740843 | 0.0071982538 |
| f__Acidaminococcaceae | 0.0167462889 | 0.0052414082 |
| f__Campylobacteraceae | 0.0159838256 | 0.0387975785 |
| f__Paludibacteraceae | 0.0158802598 | 0.0125214151 |
| f__Clostridiaceae | 0.0142082983 | 0.0159927811 |
| f__Lactobacillaceae | 0.0120870093 | 0.0141122636 |
| f__Streptococcaceae | 0.0119333963 | 0.0179222778 |
| f__Erysipelotrichaceae | 0.0108128987 | 0.0042497143 |
| f__CAG-508 | 0.0099733313 | 0.0062656103 |
| f__Acutalibacteraceae | 0.0096833683 | 0.0060436186 |
| f__UBA3663 | 0.0094777979 | 0.0192819112 |
| f__Sphaerochaetaceae | 0.0073891166 | 0.0060831038 |
| f__Mycoplasmoidaceae | 0.0057277193 | 0.0127545402 |
| f__CAG-239 | 0.0057140284 | 0.0089502266 |
| f__CAG-826 | 0.0055560044 | 0.0028667268 |
| f__Peptostreptococcaceae | 0.0049109397 | 0.0032085173 |
| f__Tannerellaceae | 0.0046155985 | 0.0026566511 |
| f__CAG-288 | 0.0040602534 | 0.0021145362 |
| f__Rhodocyclaceae | 0.0038788761 | 0.0130720725 |
| f__Anaeroplasmataceae | 0.0030394443 | 0.0025945089 |
| f__Nanosyncoccaceae | 0.0022213343 | 0.0014395316 |
| f__Succinivibrionaceae | 0.0020045919 | 0.0024676663 |
| f__Methanomethylophilaceae | 0.0019390776 | 0.0018321268 |
| f__Dialisteraceae | 0.0017391230 | 0.0032952488 |
| f__Butyricicoccaceae | 0.0017234941 | 0.0021195229 |
| f__CAG-449 | 0.0016810036 | 0.0013345102 |
| f__Pasteurellaceae | 0.0015456101 | 0.0047318494 |
| f__CAG-465 | 0.0014721087 | 0.0026676970 |
| f__Megasphaeraceae | 0.0014360764 | 0.0023501498 |
| f__RUG14156 | 0.0014014821 | 0.0014210129 |
| f__UBA1997 | 0.0013531597 | 0.0023910775 |
| f__Enterobacteriaceae | 0.0013411897 | 0.0024260041 |
| f__Burkholderiaceae_A | 0.0012406314 | 0.0006951609 |
| f__Amoebophilaceae | 0.0011667118 | 0.0023198792 |
| f__Turicibacteraceae | 0.0011425956 | 0.0007583924 |
| f__Peptococcaceae | 0.0010095801 | 0.0006944021 |
| f__Elusimicrobiaceae | 0.0007469834 | 0.0010942911 |
| f__UBA1067 | 0.0007204041 | 0.0016219643 |
| f__Fibrobacteraceae | 0.0007103462 | 0.0011143593 |
| f__Cellulosilyticaceae | 0.0005937404 | 0.0009420951 |
| f__UBA3700 | 0.0005041373 | 0.0008110409 |
| f__W3P20-009 | 0.0004944734 | 0.0006907562 |
| f__Borkfalkiaceae | 0.0003881408 | 0.0010875597 |
| f__Anaerovoracaceae | 0.0003775136 | 0.0007742000 |
| f__Veillonellaceae | 0.0003528131 | 0.0009774385 |
| f__Akkermansiaceae | 0.0003286643 | 0.0011129928 |
| f__P3 | 0.0002788056 | 0.0009614512 |
| f__Helicobacteraceae | 0.0002614012 | 0.0005556899 |
| f__Metamycoplasmataceae | 0.0002189170 | 0.0007439893 |
| f__Coprobacillaceae | 0.0002178342 | 0.0005422852 |
| f__CAG-272 | 0.0002069501 | 0.0008766710 |
| f__Rs-D84 | 0.0001918840 | 0.0007168920 |
| f__UBA1381 | 0.0001460821 | 0.0004690733 |
family_arrange <- family_summary %>%
group_by(family) %>%
summarise(mean=sum(relabun)) %>%
arrange(-mean) %>%
select(family) %>%
pull()
# Per treatment
family_summary %>%
left_join(genome_metadata %>% select(family,phylum) %>% unique(),by=join_by(family==family)) %>%
left_join(sample_metadata,by=join_by(sample==sample)) %>%
filter(family %in% family_arrange[1:20]) %>%
mutate(family=factor(family,levels=rev(family_arrange[1:20]))) %>%
filter(relabun > 0) %>%
ggplot(aes(x=relabun, y=family, group=family, color=phylum)) +
scale_color_manual(values=phylum_colors[-8]) +
geom_jitter(alpha=0.5) +
facet_grid(.~treatment)+
theme_minimal() +
labs(y="Family", x="Relative abundance", color="Phylum")
4.2.2 Genus
genus_summary <- genome_counts_filt %>%
mutate_at(vars(-genome),~./sum(.)) %>% #apply TSS nornalisation
pivot_longer(-genome, names_to = "sample", values_to = "count") %>% #reduce to minimum number of columns
left_join(sample_metadata, by = join_by(sample == sample)) %>% #append sample metadata
left_join(genome_metadata, by = join_by(genome == genome)) %>% #append genome metadata
group_by(sample,phylum,genus) %>%
summarise(relabun=sum(count)) %>%
filter(genus != "g__") %>%
mutate(genus= sub("^g__", "", genus))
genus_summary_sort <- genus_summary %>%
group_by(genus) %>%
summarise(mean=mean(relabun, na.rm=T),sd=sd(relabun, na.rm=T)) %>%
arrange(-mean)
genus_summary_sort %>%
tt()| genus | mean | sd |
|---|---|---|
| Prevotella | 3.954166e-01 | 0.1038048308 |
| Alloprevotella | 4.821648e-02 | 0.0124460045 |
| Treponema_D | 4.083877e-02 | 0.0440444319 |
| Agathobacter | 3.516244e-02 | 0.0159828646 |
| Faecousia | 2.290556e-02 | 0.0102662784 |
| Cryptobacteroides | 2.272817e-02 | 0.0089460479 |
| UBA4372 | 2.001823e-02 | 0.0110629331 |
| Phascolarctobacterium_A | 1.674629e-02 | 0.0052414082 |
| Campylobacter | 1.598383e-02 | 0.0387975785 |
| Anaerovibrio | 1.522639e-02 | 0.0065468666 |
| RF16 | 1.511332e-02 | 0.0119538706 |
| Clostridium | 1.420830e-02 | 0.0159927811 |
| W0P33-017 | 1.386459e-02 | 0.0094151963 |
| CAMCDL01 | 1.374824e-02 | 0.0079563270 |
| Streptococcus | 1.193340e-02 | 0.0179222778 |
| CAG-196 | 1.114276e-02 | 0.0072720243 |
| UBA3663 | 9.477798e-03 | 0.0192819112 |
| Lactobacillus | 9.124798e-03 | 0.0103996217 |
| COE1 | 8.670377e-03 | 0.0048120303 |
| Lachnospira | 7.757836e-03 | 0.0044411339 |
| Faecalibacterium | 7.403613e-03 | 0.0063485771 |
| Sodaliphilus | 6.259893e-03 | 0.0023821713 |
| UBA636 | 6.053954e-03 | 0.0028821164 |
| Malacoplasma_A | 5.727719e-03 | 0.0127545402 |
| Eubacterium_R | 5.688683e-03 | 0.0048884676 |
| UBA2883 | 5.630682e-03 | 0.0043630677 |
| Gemmiger | 5.545737e-03 | 0.0036125674 |
| UBA2868 | 5.302298e-03 | 0.0075776580 |
| CAG-605 | 5.103081e-03 | 0.0085460034 |
| Parabacteroides | 4.615599e-03 | 0.0026566511 |
| UBA2882 | 4.556332e-03 | 0.0078575078 |
| CAJGDV01 | 4.375272e-03 | 0.0073946242 |
| SFTJ01 | 4.357617e-03 | 0.0031853723 |
| Ornithospirochaeta | 4.318767e-03 | 0.0026875413 |
| Zag111 | 4.278245e-03 | 0.0037356591 |
| Terrisporobacter | 4.102349e-03 | 0.0027507957 |
| UMGS1585 | 3.909555e-03 | 0.0023016276 |
| SFHR01 | 3.878876e-03 | 0.0130720725 |
| CAG-533 | 3.865377e-03 | 0.0034100580 |
| Acetatifactor | 3.325740e-03 | 0.0017960296 |
| Onthovivens | 3.112364e-03 | 0.0017978526 |
| Bullifex | 3.070349e-03 | 0.0040188810 |
| Limosilactobacillus | 2.962211e-03 | 0.0040683220 |
| Bulleidia | 2.891049e-03 | 0.0017439113 |
| RUG410 | 2.854305e-03 | 0.0030288505 |
| CAG-269 | 2.829172e-03 | 0.0024341894 |
| Enterosoma | 2.799082e-03 | 0.0019378803 |
| UBA1221 | 2.726159e-03 | 0.0032665396 |
| CAJOJO01 | 2.608791e-03 | 0.0120258428 |
| UBA4334 | 2.524620e-03 | 0.0021396414 |
| CAG-303 | 2.357897e-03 | 0.0024696723 |
| Scatovivens | 2.253934e-03 | 0.0021034110 |
| CAG-485 | 2.245221e-03 | 0.0022921856 |
| UBA2834 | 2.221334e-03 | 0.0014395316 |
| Butyribacter | 2.193939e-03 | 0.0023715379 |
| UBA11957 | 2.137090e-03 | 0.0014526629 |
| Wujia | 2.062705e-03 | 0.0017014595 |
| Succinivibrio | 2.004592e-03 | 0.0024676663 |
| CAG-267 | 1.985271e-03 | 0.0069597286 |
| Anaeroplasma | 1.970164e-03 | 0.0020442006 |
| Fimenecus | 1.925273e-03 | 0.0015984100 |
| Limisoma | 1.893799e-03 | 0.0012512398 |
| Roseburia | 1.891055e-03 | 0.0019178824 |
| Onthousia | 1.780553e-03 | 0.0016792228 |
| Oliverpabstia | 1.764149e-03 | 0.0016499416 |
| UBA1712 | 1.739674e-03 | 0.0017911848 |
| Dialister | 1.739123e-03 | 0.0032952488 |
| UBA3210 | 1.681004e-03 | 0.0013345102 |
| UBA6382 | 1.668529e-03 | 0.0015786673 |
| 1XD8-76 | 1.647968e-03 | 0.0009404726 |
| Dysosmobacter | 1.636559e-03 | 0.0006376329 |
| CAG-582 | 1.619036e-03 | 0.0023101109 |
| UBA3789 | 1.554678e-03 | 0.0021954852 |
| UBA71 | 1.539428e-03 | 0.0016045421 |
| CAG-452 | 1.504396e-03 | 0.0014926048 |
| CAG-465 | 1.472109e-03 | 0.0026676970 |
| Megasphaera | 1.436076e-03 | 0.0023501498 |
| CAG-95 | 1.397961e-03 | 0.0010793714 |
| Pararoseburia | 1.370697e-03 | 0.0012356294 |
| Stercorousia | 1.351763e-03 | 0.0019389629 |
| Escherichia | 1.341190e-03 | 0.0024260041 |
| RUG14156 | 1.320438e-03 | 0.0012877631 |
| HGM13634 | 1.287840e-03 | 0.0015722660 |
| HGM10890 | 1.261172e-03 | 0.0008205742 |
| Sutterella | 1.240631e-03 | 0.0006951609 |
| Blautia_A | 1.187043e-03 | 0.0016384301 |
| Oribacterium | 1.143520e-03 | 0.0011593782 |
| Turicibacter | 1.142596e-03 | 0.0007583924 |
| Phocaeicola | 1.124783e-03 | 0.0015425034 |
| CAG-873 | 1.121972e-03 | 0.0014125215 |
| CAG-882 | 1.119737e-03 | 0.0015619435 |
| Coprococcus_A | 1.090054e-03 | 0.0010674014 |
| CAG-307 | 1.069280e-03 | 0.0009607836 |
| RUG115 | 1.050968e-03 | 0.0014226574 |
| Ventrimonas | 1.025837e-03 | 0.0026445007 |
| CAG-194 | 9.877873e-04 | 0.0011572030 |
| RGIG3102 | 9.708819e-04 | 0.0004929237 |
| Enteromonas | 9.659928e-04 | 0.0007463490 |
| CAG-245 | 9.031702e-04 | 0.0010680329 |
| Butyricicoccus_A | 8.674245e-04 | 0.0010970992 |
| Agathobaculum | 8.560696e-04 | 0.0017107271 |
| CAG-590 | 8.339065e-04 | 0.0020798200 |
| Basfia_A | 8.158406e-04 | 0.0025857850 |
| Romboutsia | 8.085906e-04 | 0.0005738447 |
| CALZFJ01 | 7.973847e-04 | 0.0005977457 |
| CALZKI01 | 7.643313e-04 | 0.0009697478 |
| MGBC100174 | 7.579825e-04 | 0.0014812246 |
| UBA1436 | 7.469834e-04 | 0.0010942911 |
| Actinobacillus_A | 7.297695e-04 | 0.0029938658 |
| CAG-632 | 7.195232e-04 | 0.0014437470 |
| Aphodocola | 6.951033e-04 | 0.0007698976 |
| Ruminococcus_E | 6.922093e-04 | 0.0008334298 |
| Blautia | 6.863243e-04 | 0.0008814138 |
| CAG-1000 | 6.658396e-04 | 0.0011250480 |
| UBA3207 | 6.566213e-04 | 0.0008392876 |
| MGBC108787 | 6.111432e-04 | 0.0008075631 |
| Clostridium_Q | 6.109169e-04 | 0.0004432668 |
| CAG-115 | 6.102927e-04 | 0.0014104650 |
| JALEVB01 | 6.085658e-04 | 0.0004062303 |
| Cellulosilyticum | 5.937404e-04 | 0.0009420951 |
| UBA7185 | 5.890955e-04 | 0.0005426874 |
| Holdemanella | 5.881670e-04 | 0.0005929724 |
| CALXSC01 | 5.868139e-04 | 0.0013578825 |
| Mediterranea | 5.783514e-04 | 0.0009685560 |
| Bariatricus | 5.678290e-04 | 0.0004912286 |
| Scatousia | 5.644188e-04 | 0.0008769630 |
| VSOB01 | 5.599855e-04 | 0.0006888622 |
| JALFVM01 | 5.507130e-04 | 0.0006101708 |
| RGIG9287 | 5.465083e-04 | 0.0024433056 |
| SIG333 | 5.445884e-04 | 0.0009002716 |
| CAG-45 | 5.338278e-04 | 0.0008164413 |
| HGM13010 | 5.258450e-04 | 0.0004502508 |
| Limivicinus | 5.253983e-04 | 0.0005487623 |
| SFRY01 | 5.246062e-04 | 0.0004813940 |
| SFJ001 | 5.180974e-04 | 0.0003930913 |
| Hallerella | 5.172076e-04 | 0.0008613899 |
| CAG-826 | 5.170304e-04 | 0.0008743808 |
| SFIE01 | 5.169742e-04 | 0.0005550785 |
| RUG11198 | 5.127886e-04 | 0.0008351012 |
| UBA3700 | 5.041373e-04 | 0.0008110409 |
| W3P20-009 | 4.944734e-04 | 0.0006907562 |
| UMGS363 | 4.929590e-04 | 0.0012273398 |
| UMGS1491 | 4.858508e-04 | 0.0005399772 |
| Aphodosoma | 4.779456e-04 | 0.0013579188 |
| Choladocola | 4.738155e-04 | 0.0004342450 |
| Scatocola | 4.604184e-04 | 0.0010371059 |
| Ruminococcus | 4.445026e-04 | 0.0006919929 |
| UBA3282 | 4.438616e-04 | 0.0005083950 |
| UMGS1994 | 4.344562e-04 | 0.0007934213 |
| UMGS1590 | 4.204847e-04 | 0.0004036875 |
| RUG705 | 4.195280e-04 | 0.0007771757 |
| UBA7173 | 4.100424e-04 | 0.0005561943 |
| UBA1783 | 4.099466e-04 | 0.0005640421 |
| Ruminococcus_C | 4.056678e-04 | 0.0004844254 |
| Methanomethylophilus | 3.996493e-04 | 0.0004802023 |
| UBA1067 | 3.983207e-04 | 0.0009244905 |
| CAG-238 | 3.775136e-04 | 0.0007742000 |
| Bacteroides_F | 3.759222e-04 | 0.0006304753 |
| RUG14891 | 3.696802e-04 | 0.0008003112 |
| JAHHSE01 | 3.672573e-04 | 0.0011485065 |
| CAG-877 | 3.558107e-04 | 0.0007632094 |
| Fusicatenibacter | 3.544812e-04 | 0.0006932089 |
| CAMBIX01 | 3.528131e-04 | 0.0009774385 |
| CALVUP01 | 3.510109e-04 | 0.0004922037 |
| UBA7050 | 3.420853e-04 | 0.0004308404 |
| Ruminiclostridium_E | 3.410333e-04 | 0.0008951955 |
| UMGS1668 | 3.388053e-04 | 0.0005266594 |
| Akkermansia | 3.286643e-04 | 0.0011129928 |
| RUG572 | 3.220834e-04 | 0.0007503658 |
| Merdicola | 3.141435e-04 | 0.0006916879 |
| Egerieousia | 3.138723e-04 | 0.0006309551 |
| UBA4951 | 3.039960e-04 | 0.0004628059 |
| UBA6398 | 3.003435e-04 | 0.0005128175 |
| W0P28-013 | 2.889906e-04 | 0.0013727816 |
| MGBC120314 | 2.861871e-04 | 0.0006231744 |
| CAKOTZ01 | 2.857955e-04 | 0.0004180249 |
| Onthomorpha | 2.788056e-04 | 0.0009614512 |
| W0P31-042 | 2.635487e-04 | 0.0003389963 |
| CAG-302 | 2.621592e-04 | 0.0006045524 |
| Helicobacter_D | 2.614012e-04 | 0.0005556899 |
| Floccifex | 2.612166e-04 | 0.0003383941 |
| JAHHTP01 | 2.592354e-04 | 0.0002896173 |
| NK4A136 | 2.416155e-04 | 0.0010312163 |
| CAZU01 | 2.408714e-04 | 0.0005713470 |
| Butyrivibrio_A | 2.279423e-04 | 0.0003667137 |
| Copromonas | 2.255607e-04 | 0.0003928410 |
| UBA710 | 2.189170e-04 | 0.0007439893 |
| Catenibacterium | 2.178342e-04 | 0.0005422852 |
| SIG301 | 2.025205e-04 | 0.0004021773 |
| Fibrobacter | 1.931386e-04 | 0.0007993952 |
| Enterousia | 1.918840e-04 | 0.0007168920 |
| HUN007 | 1.814426e-04 | 0.0005192063 |
| Ventrenecus | 1.734925e-04 | 0.0004976721 |
| CAKQTH01 | 1.731625e-04 | 0.0004666181 |
| Marvinbryantia | 1.649863e-04 | 0.0003614440 |
| Eubacterium_F | 1.637006e-04 | 0.0003477185 |
| UMGS1663 | 1.604242e-04 | 0.0005928074 |
| OMSK01 | 1.512188e-04 | 0.0007063771 |
| JALEPO01 | 1.460821e-04 | 0.0004690733 |
| Coprococcus | 1.392515e-04 | 0.0002761491 |
| Scybalousia | 1.366405e-04 | 0.0007230946 |
| Fimousia | 1.197481e-04 | 0.0006118080 |
| CAG-557 | 1.179812e-04 | 0.0007325510 |
| Clostridium_AI | 1.070752e-04 | 0.0007418386 |
| RGIG1934 | 8.794057e-05 | 0.0002976833 |
| Galligastranaerophilus_A | 8.104457e-05 | 0.0003930025 |
genus_arrange <- genus_summary %>%
group_by(genus) %>%
summarise(mean=sum(relabun)) %>%
filter(genus != "g__")%>%
arrange(-mean) %>%
select(genus) %>%
mutate(genus= sub("^g__", "", genus)) %>%
pull()
#Per treatment
genus_summary %>%
left_join(sample_metadata,by=join_by(sample==sample)) %>%
mutate(genus=factor(genus, levels=rev(genus_summary_sort %>% pull(genus)))) %>%
filter(relabun > 0) %>%
ggplot(aes(x=relabun, y=genus, group=genus, color=phylum)) +
scale_color_manual(values=phylum_colors) +
geom_jitter(alpha=0.5) +
facet_grid(.~treatment)+
theme_minimal() +
labs(y="Family", x="Relative abundance", color="Phylum")